NAME

       bamsplit - split BAM files

SYNOPSIS

       bamsplit [options]

DESCRIPTION

       bamsplit  reads  a  BAM  file  via  standard input and creates a set of output files with at most a given
       number of alignments each. The concatenation of the output files via  bamcat  restores  the  sequence  of
       alignments in the original input file. The splitting does not consider read pairs, i.e. the ends of pairs
       can end up in separate files.

       The following key=value pairs can be given:

       n=<65536>: number of alignments per output file.

       prefix=<filename> prefix for the create files. The created files will  have  names  ${prefix}_000000.bam,
       ${prefix}_000001.bam, etc.

       level=<-1|0|1|9|11>: set compression level of the output BAM file. Valid values are

       -1:    zlib/gzip default compression level

       0:     uncompressed

       1:     zlib/gzip level 1 (fast) compression

       9:     zlib/gzip level 9 (best) compression

       If libmaus has been compiled with support for igzip (see https://software.intel.com/en-us/articles/igzip-
       a-high-performance-deflate-compressor-with-optimizations-for-genomic-data) then an additional valid value
       is

       11:    igzip compression

       verbose=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <tischler@mpi-cbg.de>

COPYRIGHT

       Copyright  ©  2009-2013  German  Tischler,  © 2011-2013 Genome Research Limited.  License GPLv3+: GNU GPL
       version 3 <http://gnu.org/licenses/gpl.html>
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to  the  extent
       permitted by law.